GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvE in Desulfovibrio vulgaris Miyazaki F

Align Aromatic-amino-acid aminotransferase 1; ARAT-I; AROAT; EC 2.6.1.57 (characterized)
to candidate 8502295 DvMF_3003 putative transcriptional regulator, GntR family (RefSeq)

Query= SwissProt::H3ZPL1
         (417 letters)



>FitnessBrowser__Miya:8502295
          Length = 394

 Score =  314 bits (804), Expect = 3e-90
 Identities = 162/389 (41%), Positives = 244/389 (62%), Gaps = 16/389 (4%)

Query: 32  SEIRELLKLVETSDVISLAGGLPAPETFPVEIIGEITKEVLEKHAAQALQYGTTKGFTPL 91
           S IRE+LK+    D+IS AGGLP P +FPV+ +      VLE+   +ALQY TT+GF PL
Sbjct: 13  SYIREILKVTAQPDIISFAGGLPHPASFPVDAVASAAASVLEEAGPEALQYTTTEGFPPL 72

Query: 92  RLALAEWMRERYD---IPISKVDIMTTSGSQQALDLIGRVFINPGDIIVVEAPTYLAALQ 148
           R    +W+ +RY    I +S  DI+ T+GSQQALDL+ +  I+ G  +V+E P YL A+Q
Sbjct: 73  R----QWIADRYKRQGINVSPDDILITTGSQQALDLVAKACIDRGGRVVMERPGYLGAIQ 128

Query: 149 AFKYYEPEFVQIPLDDEGMNVDLLEEKLQELEKEGKKVKIVYTIPTFQNPAGVTMNEKRR 208
            F  + P+FV +PL   G++ D L        K     ++ Y +P+FQNP+G+T +E+ R
Sbjct: 129 CFSVFGPDFVTVPLTPRGVDTDALR-------KAATGAQVFYAVPSFQNPSGITYDEQTR 181

Query: 209 KRLLELASQYDFIIVEDNPYGELRYSGEPVKPIKAWDEEGRVIYLGTFSKILAPGFRIGW 268
           + + E+ ++   ++VEDNPYGELR+ G+ + P++A+ +   V+ LG+FSK+++PG R+GW
Sbjct: 182 REVAEIMAETGCLMVEDNPYGELRFMGQHLPPVRAYMQAPSVL-LGSFSKVVSPGLRLGW 240

Query: 269 IAAEPHFIRKLEIAKQSVDLCTNTFSQVIAWKYVEGGYLDKHIPKIIEFYKPRRDAMLKA 328
           + A    +  +  AKQ+ DL T  F+Q I  +Y+    +DKHI  I   Y  +RDAM++A
Sbjct: 241 VCAPQEVLNPMITAKQASDLHTPGFTQRILHRYLMDNDVDKHIASIRARYGAQRDAMVQA 300

Query: 329 LEEFMPDGVKWTKPEGGMFVWATLPEGIDTKLMLEKAVAKGVAYVPGEAFFAHRDVKNTM 388
           +    P+ V  T+PEGGMF+W TLPEGI  + +  KA+ + VA+VPG  F+   +  +T 
Sbjct: 301 IRRHFPEDVACTEPEGGMFLWCTLPEGISAEALFHKAIERKVAFVPGRPFYVD-ETDDTF 359

Query: 389 RLNFTYVPEEKIREGIKRLAETIKEEMKK 417
           RLNF+    E I EGI RL + ++E + K
Sbjct: 360 RLNFSNSSPELIEEGIARLGQCLREYLGK 388


Lambda     K      H
   0.318    0.137    0.398 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 459
Number of extensions: 24
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 417
Length of database: 394
Length adjustment: 31
Effective length of query: 386
Effective length of database: 363
Effective search space:   140118
Effective search space used:   140118
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory